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I recently bought a house with very dirty walls. Some of the walls have mildew and need to be cleaned with bleach. In addition there are hardwood floors throughout. Should I have the floors refinished and then clean the walls or do the walls first.
I'd do the walls first so that any mess/damage to the floors can be taken care of when the floors get redone.
Be aware that washing the surface down with bleach will only kill the surface mold, it will do nothing for any trapped mold which will continue to sprout anew on the surface over time. Make sure that whatever has caused the mold has been rectified before cleaning/painting the walls.
Normally, I liked to have the floors finished first. Floor sanding and refinishing results in dust over all the walls, stain or varnish splashed on the walls and scuff marks from the floor guys. Guess who gets to do all the cleaning and touch-up!
In your case, however, I would get rid of your mildew first. You don't want to be working over new floors with water and clorox!
After the floor is done, I would completely cover the floor with red rosin paper. This will totally protect it from dust and paint splatter. It won't protect it from heavy objects being dropped on it though. I used blue painters tape to tape the perimeter edges to the floor and regular masking tape to tape the rosin paper laps to itself. Rosin paper only costs about $12 for 500 square feet.